To this day, primary rectal cancer patient management continues to be challenged by significant problems in morbidity, locoregional recurrence, and distant organ recurrence. In most studies, rectal cancer is commingled with colon cancer, yet it is clinically treated differently and molecularly distinct. Development and verification of predictive biomarkers of primary rectal tumors could significantly improve disease outcome, reduce morbidity, and most importantly improve primary rectal tumor treatment stratification. We have identified, in preliminary pilot studies, epigenomic aberrations (promoter region methylation) of non-coding genomic repeat sequences and tumor-related genes in primary rectal adenocarcinoma that are predictive biomarkers for locoregional and distant organ metastasis recurrence and disease outcome. We propose to validate these findings in primary rectal tumors from two large-scale multicenter phase III clinical trials of patients randomized between Total Mesorectal Excision surgery(TME) versus Pre-Radiotherapy followed by TME (PRTME) in a 13 yr follow-up (retrospective study), and the prospective randomized Phase III multicenter RAPIDO clinical trial of neoadjuvant chemoradiation followed by TME. Development of rectal cancer biomarkers may improve stratification into more efficient control of primary rectal tumors with and without micrometastasis. Our objective is to develop and validate a predictive biomarker panel for utility in stratifying patients for treatment. We will identify primry rectal cancer patients who could benefit from TME alone versus different approaches of neoadjuvant treatments that include radiation alone or chemoradiation regimens. The Aims are as follows: Aim I: Validate epigenomic biomarkers of primary rectal cancer to predict distant organ recurrence in TME or PRTME treated patients. Aim II: Validate epigenomic biomarkers of primary rectal cancer to predict locoregional recurrence in TME or PRTME treated patients. Aim III: Validate optimal epigenomic rectal cancer biomarkers to predict disease-free survival in neoadjuvant chemoradiation followed by TME. The study addresses an important treatment problem of primary rectal cancer using a novel combination of epigenomic predictive biomarkers.